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File Formats

Show or hide the answer Can I save/convert microscopy files between formats with your software?

Using Bio-Formats, we support conversion from any supported format into a few different "open standard" formats including OME-TIFF. As shown on the supported formats table, you can convert from any format on the list into any format with a green checkmark in the "Export" column.

There are many ways to use Bio-Formats to convert between formats, but two easy ways are the Bio-Formats command line tools and the Bio-Formats plugins for ImageJ.

We have no plans to convert into any vendor's "closed-source" proprietary microscopy formats. Philosophically, we believe that writing to proprietary file formats reinforces the proliferation of proprietary files, and further validates vendors' continued creation of incompatible formats. Instead, we are promoting OME-TIFF as the standard, and believe the community would be best served by petitioning vendors to support OME-TIFF as at least an interchange format. Further, from a practical perspective, we have limited resources, and feel they are better served adding additional readers and fixing bugs rather than creating proprietary format writers. Lastly, the Bio-Formats writer API is open. There is nothing to stop a vendor from creating a writer for their particular format. We would even be happy to include it in Bio-Formats, if they are willing to open source their code.

Show or hide the answer How many file formats do you support?

From 4.1.x, OMERO now imports all the formats read by Bio-Formats including microscopy, HCS, tissue scanner and graphics file formats, over 120 in total. See the supported formats table for full details.

Show or hide the answer What AVI compression formats do you support?

There are a limited number of AVI input compression formats supported by Bio-Formats and thus supported by OMERO.importer:

  • MSRLE (Microsoft Run Length Encoding)
  • MS_VIDEO
  • JPEG

More compression formats are supported if you use a MOV container and have QuickTime for Java installed. However, the portability of QTJ is very limited (Mac OS X and Windows only), it has several bugs, and has been deprecated by Apple.

All these source formats are at present stored uncompressed in OMERO.server after import, so if your goal is to reduce drive space usage overall, having a compressed source movie is not going to help.

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